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Opened 4 years ago
Closed 4 years ago
#5808 closed defect (fixed)
Rotamers calls changed size() directly
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.4.dev202112170201 (2021-12-17 02:01:48 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4.dev202112170201 (2021-12-17)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\HIV2_HomoModel\HIV2A3G_HM2.cxs" format session
Log from Fri Dec 17 22:27:34 2021UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Wed Dec 15 01:35:36 2021UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sun Nov 21 18:47:37 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sun Nov 21 17:58:37 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 18:48:20 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 18:28:14 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 18:09:24 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 17:48:03 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 16:57:57 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 16:49:22 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 00:57:03 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\temp\EM data\RCM_HomoModel\rcmA3G-Vif_HM_interface 1.cxs" format
> session
Log from Sat Nov 20 00:32:32 2021UCSF ChimeraX version: 1.3rc202111162003
(2021-11-16)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:/Figures/A3GVif_meeting_20211014/A3G-Vif interface1_20211011.cxs"
Log from Wed Oct 13 00:48:41 2021UCSF ChimeraX version: 1.3.dev202109251824
(2021-09-25)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:/Figures/A3G-Vif interface1_20211011.cxs"
Log from Tue Oct 12 00:11:29 2021UCSF ChimeraX version: 1.3.dev202109251824
(2021-09-25)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\Figures\A3G-Vif interface_v1.cxs" format session
Log from Mon Oct 11 22:59:16 2021UCSF ChimeraX version: 1.3.dev202109251824
(2021-09-25)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/Krios/20210423/csrelion/6221/coot/csJ245rsr86-coot-1.pdb
Chain information for csJ245rsr86-coot-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> set bgColor white
> graphics silhouettes true
> graphics silhouettes false
> color bychain
> select #1/A:98,124-125,127-130,270, select #1/B:15,19,22,43,44,70,83
288 atoms, 287 bonds, 15 residues, 1 model selected
> style sel stick
Changed 288 atom styles
> show sel atoms
> color sel byhetero
> label #1/B:15,19,22,43,44,70,83 height 0.6 bgColor #f08080
> label #1/A:98,124-125,127-130,270 height 0.6 bgColor #aaaaff
> hide #1/C,D,E ribbons
> select clear
> ui mousemode right distance
[Repeated 1 time(s)]
> distance /B:43@HD2 /A:127@HE1
Distance between /B HIS 43 HD2 and /A TRP 127 HE1: 3.279Å
> ~distance
> select /B:48
16 atoms, 16 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color sel #fe8787 atoms
> color sel lightcoral atoms
> label #1/B:15,19,22,43,44,70,83 height 0.6 bgColor #fe8787
> ui tool show "Selection Inspector"
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> label #1/B:15,19,22,43,44,70,83 height 0.6 bgColor light pink
> label #1/B:15,19,22,43,44,70,83 height 0.6 color steel blue bgColor light
> pink
> label #1/B:15,19,22,43,44,70,83 height 0.6 color steel blue
> label #1/A:98,124-125,127-130,270 height 0.6 color steel blue bgColor
> #aaaaff
> label #1/A:98,124-125,127-130,270 height 0.6 color teal bgColor #aaaaff
> label #1/B:15,19,22,43,44,70,83 height 0.6 color teal
> label #1/B:15,19,22,43,44,70,83 height 0.6 color teal bgColor transparent
> label #1/B:15,19,22,43,44,70,83 height 0.6 color teal bgColor yellow
> ui tool show "Side View"
> label #1/A:98,124-125,127-130,270 height 0.6 color teal bgColor skyblue
> label #1/A:98,124-125,127-130,270 height 0.6 color teal bgColor powderblue
> ~label
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> hide #1
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 11 residues, 1 model selected
> style sel stick
Changed 200 atom styles
> show sel atoms
> color sel byhetero
> view sel
> graphics silhouettes true
> graphics silhouettes false
> select clear
> label #1/A:98,127-130,270 height 0.6 color teal bgColor powderblue
> label #1/A:98,127-130,270 height 0.5 color teal bgColor powderblue
> label #1/A:98,127-130,270 height 0.6 color teal bgColor powderblue
> save C:\Users\lilyy\Desktop\image2.png supersample 3
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor yellow
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor light pink
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor misty rose
> save C:\Users\lilyy\Desktop\image3.png supersample 3
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor orange
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor navajowhite
> save C:\Users\lilyy\Desktop\image2.png supersample 3
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor gold
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor navajowhite
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor yellow
> ui tool show "Selection Inspector"
> select clear
> save C:\Users\lilyy\Desktop\image3.png supersample 3
> ui mousemode right label
> ui mousemode right "move label"
> save C:\Users\lilyy\Desktop\image4.png supersample 3
> save C:\Users\lilyy\Desktop\image2.png supersample 3
> hbonds reveal true
609 hydrogen bonds found
> ~hbonds
> ~spheres
Unknown command: ~spheres
> undo
[Repeated 2 time(s)]
> select clear
> save C:\Users\lilyy\Desktop\image3.png supersample 3
> hide #1
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 11 residues, 1 model selected
> style sel stick
Changed 200 atom styles
> show sel atoms
> style sel stick
Changed 200 atom styles
> hide H
> select clear
> select /B:15@NH2
1 atom, 1 residue, 1 model selected
> select clear
> select /B:15@NH2
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
2 hydrogen bonds found
> hide H
> show H
> hide #1
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 2 pseudobonds, 11 residues, 2 models selected
> show sel cartoons
> style sel stick
Changed 200 atom styles
> color sel byhetero
> style sel stick
Changed 200 atom styles
> show sel atoms
> save C:\Users\lilyy\Desktop\image3.png supersample 3
> select clear
> select /B:83@HE21
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B GLN 83 NE2 /A ASP 130 OD1 /B GLN 83 HE21 3.452 2.722
1 hydrogen bonds found
> select clear
> hide H
> select /A:270@NZ
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select clear
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 11 residues, 1 model selected
> color sel byhetero
> select clear
> select /A:270@CB
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance /B:44@CE2 /B:44@CZ
Distance between /B TYR 44 CE2 and CZ: 1.373Å
> distance /A:270@CB /B:44@CE2
Distance between /A LYS 270 CB and /B TYR 44 CE2: 5.464Å
> hide #1
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 2 pseudobonds, 11 residues, 2 models selected
> style sel stick
Changed 200 atom styles
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
6 contacts
atom1 atom2 overlap distance
/A LYS 270 HE2 /B TYR 44 CD1 -0.248 2.948
/A LYS 270 HE2 /B TYR 44 CG -0.255 2.955
/A LYS 270 HE2 /B TYR 44 CD2 -0.360 3.060
/A LYS 270 CE /B TYR 44 CD1 -0.360 3.760
/A LYS 270 HE2 /B TYR 44 CE1 -0.379 3.079
/A LYS 270 CE /B TYR 44 CE1 -0.390 3.790
6 contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
6 contacts
atom1 atom2 overlap distance
/A LYS 270 HE2 /B TYR 44 CD1 -0.248 2.948
/A LYS 270 HE2 /B TYR 44 CG -0.255 2.955
/A LYS 270 HE2 /B TYR 44 CD2 -0.360 3.060
/A LYS 270 CE /B TYR 44 CD1 -0.360 3.760
/A LYS 270 HE2 /B TYR 44 CE1 -0.379 3.079
/A LYS 270 CE /B TYR 44 CE1 -0.390 3.790
6 contacts
> hide H
> ~distance
> save "E:/Figures/A3G-Vif interface_v1.cxs"
> select clear
> select /A:127@CZ2
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui tool show Distances
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
12 contacts
atom1 atom2 overlap distance
/A TRP 127 HD1 /B TRP 70 CH2 0.235 2.465
/A TRP 127 CD1 /B HIS 43 NE2 0.162 3.178
/A TRP 127 HD1 /B TRP 70 HH2 0.157 1.843
/A TRP 127 CD1 /B TRP 70 CH2 0.110 3.290
/A TRP 127 CD1 /B TRP 70 HH2 0.073 2.627
/A TRP 127 CD1 /B HIS 43 CE1 -0.060 3.460
/A TRP 127 CD1 /B HIS 43 CD2 -0.158 3.558
/A TRP 127 NE1 /B HIS 43 NE2 -0.200 3.465
/A TRP 127 NE1 /B HIS 43 CD2 -0.201 3.526
/A TRP 127 CG /B HIS 43 NE2 -0.205 3.545
/A TRP 127 CD1 /B TRP 70 CZ2 -0.350 3.750
/A TRP 127 CG /B HIS 43 CE1 -0.361 3.761
12 contacts
> hide H
> select /A:129@CD
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
3 contacts
atom1 atom2 overlap distance
/A PRO 129 CD /B TRP 70 CE3 -0.034 3.434
/A PRO 129 HD3 /B TRP 70 CE3 -0.142 2.842
/A PRO 129 CD /B TRP 70 CD2 -0.167 3.567
3 contacts
> hide H
> select /B:83@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select /B:15@NE
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
2 hydrogen bonds found
> select /A:98@OG1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> ui mousemode right distance
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> close #2
> hbonds /A@O* restrict /B:15 distance 3.8 reveal true name hbond
Expected a keyword
> hbonds /A@O* restrict /B:15 distance 3.8 reveal true
Expected a keyword
> hbonds /A@O* restrict /B:15 distance 3.8
Expected a keyword
> hbonds /A@O* restrict /B:15
2 hydrogen bonds found
> hbonds /A@O* restrict /B:15 reveal true
2 hydrogen bonds found
> select /B:15@HE
1 atom, 1 residue, 1 model selected
> select /A:98@OG1
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross distSlop 0.5 intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict cross distSlop 1.0 intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select /B:15@HH21
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hbonds sel restrict cross saltOnly true intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
2 hydrogen bonds found
> hbonds sel restrict cross saltOnly true intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
2 hydrogen bonds found
> ui tool show Toolbar
> toolshed show
> save "E:/Figures/A3G-Vif interface_v1.cxs"
> open E:/Krios/20210423/csrelion/6221/coot/csJ245rsr86-coot-2.pdb
Chain information for csJ245rsr86-coot-2.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide sel atoms
[Repeated 1 time(s)]
> hide #2
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker csJ245rsr86-coot-1.pdb, chain A (#1) with csJ245rsr86-coot-2.pdb,
chain A (#2), sequence alignment score = 2116.4
RMSD between 384 pruned atom pairs is 0.016 angstroms; (across all 384 pairs:
0.016)
> hide #2/C,D,E
> show #2 ribbons
> color sel bychain
> hide #!1 models
> select #2
14932 atoms, 15144 bonds, 10 pseudobonds, 915 residues, 2 models selected
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> color sel bychain
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 5 pseudobonds, 11 residues, 3 models selected
> select #2/A:98,127-130,270, select #2/B:15,43,44,70,83
200 atoms, 200 bonds, 11 residues, 1 model selected
> style sel stick
Changed 200 atom styles
> show sel atoms
> color sel byhetero
> select clear
> select #2/A:98@HG1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross saltOnly true intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict cross saltOnly true intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select clear
> select #2/B:15@HE
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross saltOnly true intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.507
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.506
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.800 1.980
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.801 1.980
4 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
csJ245rsr86-coot-1.pdb #1/B ARG 19 N csJ245rsr86-coot-2.pdb #2/B ARG 15 O csJ245rsr86-coot-1.pdb #1/B ARG 19 H 2.944 2.131
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.507
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.506
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.800 1.980
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.801 1.980
5 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
csJ245rsr86-coot-1.pdb #1/B ARG 19 N csJ245rsr86-coot-2.pdb #2/B ARG 15 O csJ245rsr86-coot-1.pdb #1/B ARG 19 H 2.944 2.131
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.507
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH1 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH12 3.200 2.506
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.800 1.980
csJ245rsr86-coot-2.pdb #2/B ARG 15 NH2 csJ245rsr86-coot-2.pdb #2/A ASP 128 OD2 csJ245rsr86-coot-2.pdb #2/B ARG 15 HH22 2.801 1.980
5 hydrogen bonds found
> select clear
> select #2/A:98@HG1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select #3
2 pseudobonds, 1 model selected
> ~select #3
Nothing selected
> close #3
> select #2/A:98@HG1
1 atom, 1 residue, 1 model selected
> select #2/A:98@HG1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
csJ245rsr86-coot-1.pdb #1/A ARG 102 N csJ245rsr86-coot-2.pdb #2/A THR 98 O csJ245rsr86-coot-1.pdb #1/A ARG 102 H 3.283 2.456
1 hydrogen bonds found
> hide H
> select #2/A:98@OG1
1 atom, 1 residue, 1 model selected
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel restrict cross relax false intraMol false intraRes false reveal
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Using precise constraint criteria
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select clear
> select #2/A:98@OG1
1 atom, 1 residue, 1 model selected
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
2 csJ245rsr86-coot-2.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #2
> show #!1 models
> select #1/A:98,127-130,270, select #1/B:15,43,44,70,83
200 atoms, 200 bonds, 3 pseudobonds, 11 residues, 2 models selected
> style sel stick
Changed 200 atom styles
> show sel atoms
> color sel byhetero
> select clear
> select #1/B:44,43,70,83,15
102 atoms, 102 bonds, 5 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
26 contacts
atom1 atom2 overlap distance
/B TRP 70 CH2 /A TRP 127 HD1 0.235 2.465
/B HIS 43 NE2 /A TRP 127 CD1 0.162 3.178
/B TRP 70 HH2 /A TRP 127 HD1 0.157 1.843
/B TRP 70 CH2 /A TRP 127 CD1 0.110 3.290
/B ARG 15 HH22 /A ASP 128 OD2 0.100 1.980
/B TRP 70 HH2 /A TRP 127 CD1 0.073 2.627
/B TRP 70 CE3 /A PRO 129 CD -0.034 3.434
/B HIS 43 CE1 /A TRP 127 CD1 -0.060 3.460
/B ARG 15 NH2 /A ASP 128 OD2 -0.096 2.801
/B TRP 70 CE3 /A PRO 129 HD3 -0.142 2.842
/B HIS 43 CD2 /A TRP 127 CD1 -0.158 3.558
/B TRP 70 CD2 /A PRO 129 CD -0.167 3.567
/B HIS 43 NE2 /A TRP 127 NE1 -0.200 3.465
/B HIS 43 CD2 /A TRP 127 NE1 -0.201 3.526
/B HIS 43 NE2 /A TRP 127 CG -0.205 3.545
/B TYR 44 CD1 /A LYS 270 HE2 -0.248 2.948
/B TYR 44 CG /A LYS 270 HE2 -0.255 2.955
/B ARG 15 CZ /A ASP 128 OD2 -0.259 3.439
/B ARG 15 CG /A LYS 99 NZ -0.302 3.627
/B TRP 70 CZ2 /A TRP 127 CD1 -0.350 3.750
/B TYR 44 CB /A LYS 270 CB -0.358 3.758
/B TYR 44 CD2 /A LYS 270 HE2 -0.360 3.060
/B TYR 44 CD1 /A LYS 270 CE -0.360 3.760
/B HIS 43 CE1 /A TRP 127 CG -0.361 3.761
/B TYR 44 CE1 /A LYS 270 HE2 -0.379 3.079
/B TYR 44 CE1 /A LYS 270 CE -0.390 3.790
26 contacts
> ~contacts
> select #1/B:44,43,70
61 atoms, 63 bonds, 3 residues, 1 model selected
> ui tool show Distances
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
22 contacts
atom1 atom2 overlap distance
/B TRP 70 CH2 /A TRP 127 HD1 0.235 2.465
/B HIS 43 NE2 /A TRP 127 CD1 0.162 3.178
/B TRP 70 HH2 /A TRP 127 HD1 0.157 1.843
/B TRP 70 CH2 /A TRP 127 CD1 0.110 3.290
/B TRP 70 HH2 /A TRP 127 CD1 0.073 2.627
/B TRP 70 CE3 /A PRO 129 CD -0.034 3.434
/B HIS 43 CE1 /A TRP 127 CD1 -0.060 3.460
/B TRP 70 CE3 /A PRO 129 HD3 -0.142 2.842
/B HIS 43 CD2 /A TRP 127 CD1 -0.158 3.558
/B TRP 70 CD2 /A PRO 129 CD -0.167 3.567
/B HIS 43 NE2 /A TRP 127 NE1 -0.200 3.465
/B HIS 43 CD2 /A TRP 127 NE1 -0.201 3.526
/B HIS 43 NE2 /A TRP 127 CG -0.205 3.545
/B TYR 44 CD1 /A LYS 270 HE2 -0.248 2.948
/B TYR 44 CG /A LYS 270 HE2 -0.255 2.955
/B TRP 70 CZ2 /A TRP 127 CD1 -0.350 3.750
/B TYR 44 CB /A LYS 270 CB -0.358 3.758
/B TYR 44 CD2 /A LYS 270 HE2 -0.360 3.060
/B TYR 44 CD1 /A LYS 270 CE -0.360 3.760
/B HIS 43 CE1 /A TRP 127 CG -0.361 3.761
/B TYR 44 CE1 /A LYS 270 HE2 -0.379 3.079
/B TYR 44 CE1 /A LYS 270 CE -0.390 3.790
22 contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
22 contacts
atom1 atom2 overlap distance
/B TRP 70 CH2 /A TRP 127 HD1 0.235 2.465
/B HIS 43 NE2 /A TRP 127 CD1 0.162 3.178
/B TRP 70 HH2 /A TRP 127 HD1 0.157 1.843
/B TRP 70 CH2 /A TRP 127 CD1 0.110 3.290
/B TRP 70 HH2 /A TRP 127 CD1 0.073 2.627
/B TRP 70 CE3 /A PRO 129 CD -0.034 3.434
/B HIS 43 CE1 /A TRP 127 CD1 -0.060 3.460
/B TRP 70 CE3 /A PRO 129 HD3 -0.142 2.842
/B HIS 43 CD2 /A TRP 127 CD1 -0.158 3.558
/B TRP 70 CD2 /A PRO 129 CD -0.167 3.567
/B HIS 43 NE2 /A TRP 127 NE1 -0.200 3.465
/B HIS 43 CD2 /A TRP 127 NE1 -0.201 3.526
/B HIS 43 NE2 /A TRP 127 CG -0.205 3.545
/B TYR 44 CD1 /A LYS 270 HE2 -0.248 2.948
/B TYR 44 CG /A LYS 270 HE2 -0.255 2.955
/B TRP 70 CZ2 /A TRP 127 CD1 -0.350 3.750
/B TYR 44 CB /A LYS 270 CB -0.358 3.758
/B TYR 44 CD2 /A LYS 270 HE2 -0.360 3.060
/B TYR 44 CD1 /A LYS 270 CE -0.360 3.760
/B HIS 43 CE1 /A TRP 127 CG -0.361 3.761
/B TYR 44 CE1 /A LYS 270 HE2 -0.379 3.079
/B TYR 44 CE1 /A LYS 270 CE -0.390 3.790
22 contacts
> hide H
> select clear
> select #1/B:83,15
41 atoms, 39 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
/B GLN 83 NE2 /A ASP 130 OD1 /B GLN 83 HE21 3.452 2.722
3 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
/B GLN 83 NE2 /A ASP 130 OD1 /B GLN 83 HE21 3.452 2.722
3 hydrogen bonds found
> ui mousemode right label
> ui mousemode right "move label"
> select clear
> select /A:128@OD1
1 atom, 1 residue, 1 model selected
> select /A:128@OD1
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right distance
[Repeated 1 time(s)]
> distance /B:70@NE1 /A:128@OD1
Distance between /B TRP 70 NE1 and /A ASP 128 OD1: 3.896Å
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> ~distance /B:15@HE /A:98@OG1
> distance /B:15@HH21 /A:98@OG1
Distance between /B ARG 15 HH21 and /A THR 98 OG1: 4.573Å
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> ~distance /B:15@HE /A:98@OG1
> distance /B:15@HH21 /A:98@OG1
Distance already exists; modify distance properties with 'distance style'
> close #2
> select /A:128@CG
1 atom, 1 residue, 1 model selected
> select clear
> select /A:128@OD1
1 atom, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select clear
> select #1/B:44,43,70
61 atoms, 63 bonds, 3 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
22 contacts
atom1 atom2 overlap distance
/B TRP 70 CH2 /A TRP 127 HD1 0.235 2.465
/B HIS 43 NE2 /A TRP 127 CD1 0.162 3.178
/B TRP 70 HH2 /A TRP 127 HD1 0.157 1.843
/B TRP 70 CH2 /A TRP 127 CD1 0.110 3.290
/B TRP 70 HH2 /A TRP 127 CD1 0.073 2.627
/B TRP 70 CE3 /A PRO 129 CD -0.034 3.434
/B HIS 43 CE1 /A TRP 127 CD1 -0.060 3.460
/B TRP 70 CE3 /A PRO 129 HD3 -0.142 2.842
/B HIS 43 CD2 /A TRP 127 CD1 -0.158 3.558
/B TRP 70 CD2 /A PRO 129 CD -0.167 3.567
/B HIS 43 NE2 /A TRP 127 NE1 -0.200 3.465
/B HIS 43 CD2 /A TRP 127 NE1 -0.201 3.526
/B HIS 43 NE2 /A TRP 127 CG -0.205 3.545
/B TYR 44 CD1 /A LYS 270 HE2 -0.248 2.948
/B TYR 44 CG /A LYS 270 HE2 -0.255 2.955
/B TRP 70 CZ2 /A TRP 127 CD1 -0.350 3.750
/B TYR 44 CB /A LYS 270 CB -0.358 3.758
/B TYR 44 CD2 /A LYS 270 HE2 -0.360 3.060
/B TYR 44 CD1 /A LYS 270 CE -0.360 3.760
/B HIS 43 CE1 /A TRP 127 CG -0.361 3.761
/B TYR 44 CE1 /A LYS 270 HE2 -0.379 3.079
/B TYR 44 CE1 /A LYS 270 CE -0.390 3.790
22 contacts
> contacts sel restrict cross intraMol false reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
22 contacts
atom1 atom2 overlap distance
/B TRP 70 CH2 /A TRP 127 HD1 0.235 2.465
/B HIS 43 NE2 /A TRP 127 CD1 0.162 3.178
/B TRP 70 HH2 /A TRP 127 HD1 0.157 1.843
/B TRP 70 CH2 /A TRP 127 CD1 0.110 3.290
/B TRP 70 HH2 /A TRP 127 CD1 0.073 2.627
/B TRP 70 CE3 /A PRO 129 CD -0.034 3.434
/B HIS 43 CE1 /A TRP 127 CD1 -0.060 3.460
/B TRP 70 CE3 /A PRO 129 HD3 -0.142 2.842
/B HIS 43 CD2 /A TRP 127 CD1 -0.158 3.558
/B TRP 70 CD2 /A PRO 129 CD -0.167 3.567
/B HIS 43 NE2 /A TRP 127 NE1 -0.200 3.465
/B HIS 43 CD2 /A TRP 127 NE1 -0.201 3.526
/B HIS 43 NE2 /A TRP 127 CG -0.205 3.545
/B TYR 44 CD1 /A LYS 270 HE2 -0.248 2.948
/B TYR 44 CG /A LYS 270 HE2 -0.255 2.955
/B TRP 70 CZ2 /A TRP 127 CD1 -0.350 3.750
/B TYR 44 CB /A LYS 270 CB -0.358 3.758
/B TYR 44 CD2 /A LYS 270 HE2 -0.360 3.060
/B TYR 44 CD1 /A LYS 270 CE -0.360 3.760
/B HIS 43 CE1 /A TRP 127 CG -0.361 3.761
/B TYR 44 CE1 /A LYS 270 HE2 -0.379 3.079
/B TYR 44 CE1 /A LYS 270 CE -0.390 3.790
22 contacts
> hide H
> select clear
> select #1/B:83,15
41 atoms, 39 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
/B GLN 83 NE2 /A ASP 130 OD1 /B GLN 83 HE21 3.452 2.722
3 hydrogen bonds found
> hbonds sel restrict cross intraMol false intraRes false reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 csJ245rsr86-coot-1.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ARG 15 NH1 /A ASP 128 OD2 /B ARG 15 HH12 3.200 2.506
/B ARG 15 NH2 /A ASP 128 OD2 /B ARG 15 HH22 2.801 1.980
/B GLN 83 NE2 /A ASP 130 OD1 /B GLN 83 HE21 3.452 2.722
3 hydrogen bonds found
> ui mousemode right distance
> distance /A:128@CG /B:15@HE
Distance between /A ASP 128 CG and /B ARG 15 HE: 6.330Å
> close #2
> ui mousemode right distance
> select clear
> distance /A:98@OG1 /B:15@HE
Distance between /A THR 98 OG1 and /B ARG 15 HE: 3.688Å
> distance /B:70@NE1 /A:128@OD1
Distance between /B TRP 70 NE1 and /A ASP 128 OD1: 3.896Å
> ~distance
> ui mousemode right distance
> distance /B:70@NE1 /A:128@OD1
Distance between /B TRP 70 NE1 and /A ASP 128 OD1: 3.896Å
> ui mousemode right distance
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> hide #2.1 models
> save "E:/Figures/A3G-Vif interface_v1.cxs"
——— End of log from Mon Oct 11 22:59:16 2021 ———
opened ChimeraX session
> select /B:15@HE
1 atom, 1 residue, 1 model selected
> select /A:98@OG1
1 atom, 1 residue, 1 model selected
> distance /B:15@HE /A:98@OG1
Distance already exists; modify distance properties with 'distance style'
> distance /B:15@HE/A:98@OG1
Distance already exists; modify distance properties with 'distance style'
> select clear
> select /B:15@HE
1 atom, 1 residue, 1 model selected
> select clear
> help help:user
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> ui mousemode right distance
[Repeated 1 time(s)]
> distance /B:70@NE1 /A:128@OD1
Distance between /B TRP 70 NE1 and /A ASP 128 OD1: 3.896Å
> hide #2.1 models
> select /A:98@OG1
1 atom, 1 residue, 1 model selected
> select add /B:15@HE
2 atoms, 2 residues, 1 model selected
> select subtract /B:15@HE
1 atom, 1 residue, 1 model selected
> select clear
> select /B:15@HE
1 atom, 1 residue, 1 model selected
> select add /A:98@OG1
2 atoms, 2 residues, 1 model selected
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> ~distance /B:15@HE /A:98@OG1
> select clear
> help help:user
> distance /B:15@HE' /A:98@OG1
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
1
> distance /B:15@HE' /A:98@OG1 reveal true
Expected a keyword
> distance /B:15@HE' /A:98@OG1 name weakHbond
Expected a keyword
> distance /B:15@HE /A:98@OG1
Distance between /B ARG 15 HE and /A THR 98 OG1: 3.688Å
> ui mousemode right distance
> ui mousemode right "tape measure"
> marker segment #4 position 152.8,145.7,130.4 toPosition 155.7,143.6,129.6
> color yellow radius 0.1 label 3.688 labelHeight 0.3688 labelColor yellow
> close #4
> marker segment #4 position 154.9,146.5,129.8 toPosition 155.7,143.6,129.6
> color yellow radius 0.1 label 3.054 labelHeight 0.3054 labelColor yellow
> close #4
> select /B:15@HE
1 atom, 1 residue, 1 model selected
> select add /A:98@OG1
2 atoms, 2 residues, 1 model selected
> select subtract /A:98@OG1
1 atom, 1 residue, 1 model selected
> color sel cyan
> select clear
> ui tool show "Selection Inspector"
> select clear
> color sel #00bfff
> select clear
[Repeated 1 time(s)]
> color sel cyan
> select clear
> color sel #00bfff
[Repeated 1 time(s)]
> select clear
> save C:\Users\lilyy\Desktop\image2.png supersample 3
> save "E:/Figures/A3G-Vif interface_v1.cxs"
——— End of log from Tue Oct 12 00:11:29 2021 ———
opened ChimeraX session
> ui mousemode right distance
> distance /A:130@OD1 /B:15@HH12
Distance between /A ASP 130 OD1 and /B ARG 15 HH12: 3.304Å
> select clear
> ui tool show "Selection Inspector"
> color sel #00bfff
> save C:\Users\lilyy\Desktop\image1.png supersample 3
> save "E:/Figures/A3G-Vif interface1_20211011.cxs"
——— End of log from Wed Oct 13 00:48:41 2021 ———
opened ChimeraX session
> open "E:/temp/EM data/RCM_HomoModel/rcmA3GVifCbfb_HM5-coot-1.pdb"
Chain information for rcmA3GVifCbfb_HM5-coot-1.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 00:32:32 2021 ———
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> hide #3 models
> show #3 models
> show #!2 models
> show #!1 models
> hide #4 models
> select #1/A:99@CG
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!1 models
> show #4 models
> select #4/B:16,17,45,46,74,86
130 atoms, 131 bonds, 6 residues, 1 model selected
> style sel stick
Changed 130 atom styles
> show sel atoms
> show #!1 models
> hide #!1 models
> select #4/A:58,59,65,98,127,128,129,130,270
162 atoms, 162 bonds, 9 residues, 1 model selected
> style sel stick
Changed 162 atom styles
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 00:57:03 2021 ———
opened ChimeraX session
> select clear
> show #!1 models
> hide #!1 models
> color #4/B #a8b783
> color #4/A #deb887
> select #4/A:58,59,65,98,127,128,129,130,270
162 atoms, 162 bonds, 9 residues, 1 model selected
> style sel stick
Changed 162 atom styles
> color sel byhetero
> select #4/B:16,17,45,46,74,86
130 atoms, 131 bonds, 6 residues, 1 model selected
> color sel byhetero
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #4 models
> show #!1 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
> show #!1 models
> hide #4 models
> hide #!1 models
> show #4 models
> hide H
> show #!1 models
> hide #4 models
> show #4 models
> hide #!1 models
> hide #4 models
> show #!1 models
> ui tool show "Selection Inspector"
> select clear
> hide #!1 models
> show #4 models
> label #4/A:58,59,65,98,127,128,129,130,270 height 1 bgColor green
> show #!1 models
> hide #!1 models
> label #4/A:58,59,65,98,127,128,129,130,270 height 0.5 bgColor green
> show #!1 models
> hide #!1 models
> label #4/A:58,59,65,98,127,128,129,130,270 height 0.8 bgColor green
> show #!1 models
> hide #!1 models
> label #4/A:58,59,65,98,127,128,129,130,270 height 0.6 bgColor green
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Selection Inspector"
> select #4/A:131
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color sel #9a7f5e atoms
> label #4/A:58,59,65,98,127,128,129,130,270 height 0.6 bgColor #9a7f5e
> ui tool show "Selection Inspector"
> color sel #99aa77 atoms
> color sel burlywood atoms
> select clear
> ui mousemode right translate
> ui mousemode right "move label"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 16:49:22 2021 ———
opened ChimeraX session
> label #4/B:16,17,45,46,74,86 height 0.6 color white bgColor #55aa00
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!1 models
> ui mousemode right "move label"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 16:57:57 2021 ———
opened ChimeraX session
> select #4/A:98@OG1
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
> select #4/B:17@NH2
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select #4/B:16@HH22
1 atom, 1 residue, 1 model selected
> select #4/A:16,17
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #4/A:16,17
39 atoms, 39 bonds, 2 residues, 1 model selected
> select #4/B:16,17
48 atoms, 47 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
9 hydrogen bonds found
> select clear
> delete pseudobonds sel
[Repeated 2 time(s)]
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 17:48:03 2021 ———
opened ChimeraX session
> select #4/B:16,17,45,46,74,86
130 atoms, 131 bonds, 6 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
44 contacts
atom1 atom2 overlap distance
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 HH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ1 0.972 1.028
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 HH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 NZ 0.826 1.799
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HE2 0.572 1.428
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 NE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HE2 0.370 2.255
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CE 0.346 2.354
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 NE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CE 0.332 2.993
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 HD1 0.195 2.505
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 OH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ1 0.194 1.906
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 OH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A ASP 130 CG 0.193 3.007
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CZ2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HD2 0.187 2.513
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 NE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 NZ 0.177 3.073
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B HIS 45 NE2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 CD1 0.131 3.194
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 NE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ3 0.088 2.537
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CZ2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CD 0.069 3.331
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 16 HH22 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A THR 98 CB 0.061 2.639
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 OH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A ASP 130 OD2 0.054 2.526
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 NH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A VAL 58 O 0.050 2.655
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B HIS 45 CD2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 CD1 0.045 3.355
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 OH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 NZ 0.014 2.711
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 HD1 -0.006 2.006
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 HH22 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A VAL 58 O -0.007 2.087
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B HIS 45 NE2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 CG -0.023 3.348
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 CZ rcmA3GVifCbfb_HM5-coot-1.pdb #4/A VAL 58 O -0.049 3.229
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 CD1 -0.055 3.455
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B PHE 46 CG rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 270 CG -0.058 3.458
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 CZ rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ1 -0.062 2.762
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 HH12 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TYR 59 HA -0.063 2.063
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TYR 86 HH rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ3 -0.077 2.077
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 NH1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TYR 59 HA -0.086 2.711
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HE1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 NZ -0.090 2.715
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HD2 -0.093 2.793
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CD1 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 HZ3 -0.115 2.815
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B PHE 46 CG rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 270 HG3 -0.116 2.816
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B PHE 46 CD2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 270 HG3 -0.123 2.823
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 17 HH21 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A CYS 97 HG -0.136 2.136
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 16 NH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A THR 98 CB -0.143 3.468
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HH2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 CD1 -0.152 2.852
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B PHE 46 CB rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 270 HG2 -0.169 2.869
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CE -0.174 3.574
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CZ2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A TRP 127 HD1 -0.183 2.883
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE3 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A PRO 129 HD2 -0.183 2.883
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B ARG 16 HH22 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A THR 98 OG1 -0.191 2.291
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CD -0.197 3.597
rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 HZ2 rcmA3GVifCbfb_HM5-coot-1.pdb #4/A LYS 128 CD -0.199 2.899
44 contacts
> hide H
> select clear
> delete pseudobonds sel
[Repeated 4 time(s)]
> select #4/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> hide sel atoms
> show sel atoms
> hide H
> style sel stick
Changed 22 atom styles
> show sel atoms
> select clear
> delete pseudobonds sel
[Repeated 6 time(s)]
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
> select clear
> select #4/A:130,98
26 atoms, 24 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
9 hydrogen bonds found
> delete pseudobonds sel
[Repeated 2 time(s)]
> select clear
> delete pseudobonds sel
> select #4/B:86@OH
1 atom, 1 residue, 1 model selected
> select clear
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 18:09:24 2021 ———
opened ChimeraX session
> select #4/B:17@NH1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:17@CZ
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> select #4/B:17@HH12
1 atom, 1 residue, 1 model selected
> select clear
> select #4/B:17@NH1
1 atom, 1 residue, 1 model selected
> select #4/B:17@NH1
1 atom, 1 residue, 1 model selected
> select #4/B:17@NH1
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color =sel deepskyblue pseudobonds
> select #4/B:17@HH12
1 atom, 1 residue, 1 model selected
> select clear
> ui tool show "Selection Inspector"
> color =sel deepskyblue pseudobonds
> ui tool show "Selection Inspector"
> color =sel deepskyblue pseudobonds
> ui tool show "Selection Inspector"
> color =sel deepskyblue pseudobonds
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> ui tool show "Selection Inspector"
> select clear
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
> ui mousemode right distance
> distance #4/B:74@CE3 #4/A:129@CG
Distance between rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE3 and /A PRO 129
CG: 4.300Å
> delete pseudobonds sel
> ui mousemode right distance
> distance #4/B:74@CE3 #4/A:129@CD
Distance between rcmA3GVifCbfb_HM5-coot-1.pdb #4/B TRP 74 CE3 and /A PRO 129
CD: 3.874Å
> select clear
[Repeated 1 time(s)]
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel #00aa00 pseudobonds
> select clear
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!4 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 18:28:14 2021 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> select clear
> show #2.1 models
> hide #2.1 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.007
Changed 1 pseudobond radii
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> ui tool show "Selection Inspector"
> select clear
> ui mousemode right distance
> distance #1/A:128@OD2 #1/B:15@HH22
Distance between csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 and /B ARG 15 HH22:
1.980Å
> distance #1/B:15@HH12 #1/A:128@OD2
Distance between csJ245rsr86-coot-1.pdb #1/B ARG 15 HH12 and /A ASP 128 OD2:
2.506Å
> distance #1/A:130@OD1 #1/B:83@NE2
Distance between csJ245rsr86-coot-1.pdb #1/A ASP 130 OD1 and /B GLN 83 NE2:
3.452Å
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> ~distance #1/A:130@OD1 #1/B:83@NE2
> distance #1/B:83@NE2 #1/A:130@OD2
Distance between csJ245rsr86-coot-1.pdb #1/B GLN 83 NE2 and /A ASP 130 OD2:
4.095Å
> ~distance #1/B:83@NE2 #1/A:130@OD2
> select #1/B:83@CD
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
> select clear
> hide #!1 models
> show #!1 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> select #4/A:130@OD1
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select clear
> select #4/B:16@HH12
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> select #4/A:130@OD1
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select #4/B:16@HH12
1 atom, 1 residue, 1 model selected
> select #4/B:16, select #4/A:130
36 atoms, 34 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
9 hydrogen bonds found
> select clear
[Repeated 1 time(s)]
> show #!1 models
> hide #3 models
> show #3 models
> hide #!4 models
> show #!4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!4 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> ui tool show "Selection Inspector"
[Repeated 1 time(s)]
> color =sel deepskyblue pseudobonds
> ui tool show "Selection Inspector"
> color =sel deepskyblue pseudobonds
> select clear
> hide #!1 models
> show #!4 models
> show #3 models
> delete pseudobonds sel
[Repeated 1 time(s)]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> ui mousemode right distance
[Repeated 1 time(s)]
> distance #1/A:130@OD1 #1/B:83@HE21
Distance between csJ245rsr86-coot-1.pdb #1/A ASP 130 OD1 and /B GLN 83 HE21:
2.722Å
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> select clear
> ui tool show "Selection Inspector"
[Repeated 1 time(s)]
> color =sel deepskyblue pseudobonds
> select clear
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
> show #!1 models
> hide #!4 models
> save C:\Users\lilyy\Desktop\image1.png supersample 3
> hide #4.2 models
> show #4.2 models
> hide #!1 models
> save C:\Users\lilyy\Desktop\image2.png supersample 3
> select clear
> delete pseudobonds sel
> show #!1 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sat Nov 20 18:48:20 2021 ———
opened ChimeraX session
> hide #!4 models
> show #!1 models
> setattr #1/B:43-45 res ss_type 1
Assigning ss_type attribute to 3 items
> save A3G-Vif interface 1.pdb #1
Cannot determine format for 'A3G-Vif'
> save C:\Users\lilyy\Desktop\image1.png supersample 3
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sun Nov 21 17:58:37 2021 ———
opened ChimeraX session
> hide #!1 models
> show #!4 models
> ui mousemode right distance
> distance #4/A:130@OD1 #4/B:16@HH12
Distance between rcmA3GVifCbfb_HM5-coot-1.pdb #4/A ASP 130 OD1 and /B ARG 16
HH12: 2.640Å
> hide #3 models
> show #3 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> ui tool show "Selection Inspector"
[Repeated 1 time(s)]
> color =sel deepskyblue pseudobonds
> select clear
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Sun Nov 21 18:47:37 2021 ———
opened ChimeraX session
> open "E:\temp\EM data\AGMtan_HomoModel\AGMtanA3GVifCbfb_HM1-coot0.pdb"
> format pdb
Chain information for AGMtanA3GVifCbfb_HM1-coot0.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #5 models
> show #!1 models
> hide #!4 models
> setattr #1/B:52-59 res ss_type 2
Assigning ss_type attribute to 8 items
> setattr #1/B:51 res ss_type 0
Assigning ss_type attribute to 1 item
> close #5
> show #!4 models
> hide #!1 models
> save "E:/temp/EM data/RCM_HomoModel/rcmA3G-Vif_HM_interface 1.cxs"
——— End of log from Wed Dec 15 01:35:36 2021 ———
opened ChimeraX session
> hide #!4 models
> show #!1 models
> open "E:/temp/EM data/HIV2_HomoModel/HIV2VifCBFbhA3G_HM2-coot0.pdb"
Chain information for HIV2VifCBFbhA3G_HM2-coot0.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> show #!1 models
> hide #5 models
> hide #3 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #5 models
> select #1/B:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 8 residues, 1 model selected
> select up
2920 atoms, 2966 bonds, 177 residues, 1 model selected
Alignment identifier is 1/B
> select clear
> hide #!1 models
> show #5 models
> select #5/B:54
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
148 atoms, 149 bonds, 9 residues, 1 model selected
Alignment identifier is 5/B
> show #!1 models
> select #1/B:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 8 residues, 1 model selected
Alignment identifier is 1/B
> select clear
[Repeated 1 time(s)]
> select #1/B:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!1 models
> select #5/B:54
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
148 atoms, 149 bonds, 9 residues, 1 model selected
> select clear
> select #5/B:55
11 atoms, 10 bonds, 1 residue, 1 model selected
Alignment identifier is 5/B
> setattr #5/B:53 res ss_type 0
Assigning ss_type attribute to 1 item
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> select #5/B:44,45,46,47,49,51
120 atoms, 123 bonds, 6 residues, 1 model selected
> select #5/B:44,45,46,47
72 atoms, 73 bonds, 4 residues, 1 model selected
> select #5/B:44,45,46
56 atoms, 57 bonds, 3 residues, 1 model selected
> style sel stick
Changed 56 atom styles
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #5/A:270
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
113 atoms, 112 bonds, 7 residues, 1 model selected
> style sel stick
Changed 113 atom styles
> show sel atoms
> select clear
> select #5/B:71
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 5/B
> select #5/B:41
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:41-45
85 atoms, 88 bonds, 5 residues, 1 model selected
> hide #5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #!1 models
> show #5 models
> show #!1 models
> hide #!1 models
> select #5/B:44,45,46,73,74
94 atoms, 96 bonds, 5 residues, 1 model selected
> style sel stick
Changed 94 atom styles
> show sel atoms
> select #5/B:44,45,46,73,74,82-86
167 atoms, 169 bonds, 10 residues, 1 model selected
> style sel stick
Changed 167 atom styles
> show sel atoms
> show #!1 models
> hide #!1 models
> select #5/B:44,45,46,73,74,82-86
167 atoms, 169 bonds, 10 residues, 1 model selected
> hide sel atoms
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #5 models
> hide #!1 models
> show #5 models
> style sel stick
Changed 167 atom styles
> show sel atoms
> hide sel atoms
> select #5/B:44,45,46,49,73,74,82-86
191 atoms, 194 bonds, 11 residues, 1 model selected
> style sel stick
Changed 191 atom styles
> show sel atoms
> hide sel atoms
> select #5/B:44,45,46,49,73,74,48
125 atoms, 128 bonds, 7 residues, 1 model selected
> style sel stick
Changed 125 atom styles
> show sel atoms
> select #5/B:44,45,46,49,73,74,48
125 atoms, 128 bonds, 7 residues, 1 model selected
> hide #5 models
> show #!1 models
> hide #!1 models
> show #5 models
> show #!1 models
> hide #!1 models
> hide sel atoms
> select #5
12974 atoms, 13167 bonds, 781 residues, 1 model selected
> hide sel atoms
> select #5/A:270,125,127-130,272
117 atoms, 117 bonds, 7 residues, 1 model selected
> style sel stick
Changed 117 atom styles
> show sel atoms
> select #5/B:44-46,20,85,73,49
140 atoms, 142 bonds, 7 residues, 1 model selected
> style sel stick
Changed 140 atom styles
> show sel atoms
> show #!1 models
> hide #5 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #5
12974 atoms, 13167 bonds, 781 residues, 1 model selected
> hide H #5
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide H sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide H
> hide #5 models
> show #!1 models
> show #5 models
> hide #!1 models
> hide #5 models
> show #!1 models
> show #5 models
> hide #!1 models
> show #!4 models
> hide #5 models
> select #4/B:20
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select clear
> show #5 models
> color #5/B #a8b783
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #5 models
> select #4/A:131
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> show #5 models
> hide #!4 models
> color #5/A #deb887
> select #5/B:44-46,20,85,73,49
140 atoms, 142 bonds, 7 residues, 1 model selected
> color sel byhetero
> select #5/A:270,125,127-130,272
117 atoms, 117 bonds, 7 residues, 1 model selected
> color sel byhetero
> show #!1 models
> hide #5 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #5 models
> hide #!1 models
> show #5 models
> hide #5 models
> show #!1 models
> hide #!1 models
> show #5 models
> ui mousemode right distance
> distance #5/B:85@OH #5/A:130@OD2
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TYR 85 OH and /A ASP 130
OD2: 2.532Å
> distance #5/A:128@OD2 #5/B:85@OH
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A ASP 128 OD2 and /B TYR 85
OH: 3.328Å
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
4 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.216 2.484
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD 0.150 3.250
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 -0.018 2.718
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB -0.036 3.436
4 contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
6 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 0.391 2.309
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 0.307 1.693
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 0.287 2.413
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 0.176 1.824
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CE 0.087 2.613
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 NZ -0.189 2.814
6 contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #5/A:129@CD
1 atom, 1 residue, 1 model selected
> select #5/A:127@CZ2
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 0.466 2.874
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 0.256 3.144
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CH2 0.048 2.652
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CG HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 0.020 3.320
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 -0.012 2.652
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 -0.070 2.770
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CH2 -0.098 3.498
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 NE1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 -0.132 3.457
8 contacts
> select clear
> select #5/A:270@CD
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
12 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD 0.391 2.309
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.307 1.693
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB 0.287 2.413
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.216 2.484
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 0.176 1.824
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD 0.150 3.250
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CE HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.087 2.613
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 -0.018 2.718
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB -0.036 3.436
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CG -0.068 2.768
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HB3 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB3 -0.156 2.156
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 NZ HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 -0.189 2.814
12 contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select #5/A:270@CD
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
12 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD 0.391 2.309
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.307 1.693
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB 0.287 2.413
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.216 2.484
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 0.176 1.824
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD 0.150 3.250
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CE HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 0.087 2.613
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB2 -0.018 2.718
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 CD HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CB -0.036 3.436
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HD2 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CG -0.068 2.768
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 HB3 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HB3 -0.156 2.156
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A LYS 270 NZ HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 HD2 -0.189 2.814
12 contacts
> select #5/A:127@CE2
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 0.466 2.874
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 0.256 3.144
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CH2 0.048 2.652
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CG HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 0.020 3.320
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 -0.012 2.652
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 HD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 -0.070 2.770
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 CD1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CH2 -0.098 3.498
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 NE1 HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 CD2 -0.132 3.457
8 contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
No atoms match given atom specifier
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> hide H
> ui mousemode right distance
> distance #5/B:45@NE2 #5/A:127@CG
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 45 NE2 and /A TRP 127
CG: 3.320Å
> select #5/B:44@CE1
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.2 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.2
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict cross overlapCutoff -0.1 interModel false intraMol
> false select true reveal true log true
No atoms match given atom specifier
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> contacts sel restrict cross overlapCutoff -0.1 interModel false intraMol
> false select true reveal true log true
Allowed overlap: -0.1
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select #5/B:44@CE1
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #5/B:73@CH2 #5/A:127@CD1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CH2 and /A TRP 127
CD1: 3.498Å
> distance #5/B:73@CZ2 #5/A:129@CD
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 CZ2 and /A PRO 129
CD: 5.166Å
> ui mousemode right distance
> distance #5/B:46@CD #5/A:270@CD
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B LYS 46 CD and /A LYS 270
CD: 3.250Å
> distance #5/A:272@OD2 #5/B:49@NE1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A ASP 272 OD2 and /B TRP 49
NE1: 2.914Å
> ~distance #5/A:272@OD2 #5/B:49@NE1
> distance #5/A:272@OD1 #5/B:49@NE1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A ASP 272 OD1 and /B TRP 49
NE1: 4.930Å
> ~distance #5/A:272@OD1 #5/B:49@NE1
> distance #5/A:272@OD2 #5/B:49@NE1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A ASP 272 OD2 and /B TRP 49
NE1: 2.914Å
> select #5/B:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/B:41
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:41
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/B:41
21 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 21 atom styles
> show sel atoms
> hide sel atoms
> style sel stick
Changed 21 atom styles
> show sel atoms
> hide sel atoms
> nucleotides sel tube/slab shape box
> ui mousemode right distance
> distance #5/B:44@NE2 #5/A:127@CD1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 44 NE2 and /A TRP 127
CD1: 6.934Å
> ~distance #5/B:44@NE2 #5/A:127@CD1
> distance #5/B:44@CE1 #5/B:44@NE2
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 44 CE1 and NE2: 1.322Å
> distance #5/A:127@NE1 #5/B:44@NE2
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/A TRP 127 NE1 and /B HIS 44
NE2: 5.862Å
> ~distance #5/A:127@NE1 #5/B:44@NE2
> ui mousemode right distance
> distance #5/B:44@NE2 #5/A:127@CD1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B HIS 44 NE2 and /A TRP 127
CD1: 6.934Å
> ~distance #5/B:44@NE2 #5/A:127@CD1
> select #5/B:71
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select #5/B:44,45,46,49,73,74,48
125 atoms, 128 bonds, 1 pseudobond, 7 residues, 2 models selected
> select #5/B:44,45,46,49,73,74,48
125 atoms, 128 bonds, 1 pseudobond, 7 residues, 2 models selected
> select #5/B:44-46,20,85,73,49
140 atoms, 142 bonds, 1 pseudobond, 7 residues, 2 models selected
> select #5/B:44-46,20,85,73,49
140 atoms, 142 bonds, 1 pseudobond, 7 residues, 2 models selected
> ui tool show "Selection Inspector"
> select #5/B:72
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #a8b783
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor green
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> ui tool show "Selection Inspector"
> color sel #859168 atoms
> select #5/B:86
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select #5/B:71
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #5/B:72
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #a8b783 atoms
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #859168
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor green
> ui tool show "Selection Inspector"
> select clear
> ui mousemode right "move label"
> ui tool show "Selection Inspector"
> label #5/A:270,125,127-130,272 height 0.6 white color brown
Expected a keyword
> label #5/A:270,125,127-130,272 height 0.6 color white bgColor brown
> select #5/A:131
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color sel #997e5d atoms
> color sel #ddeebb atoms
> color sel burlywood atoms
> label #5/A:270,125,127-130,272 height 0.6 color white bgColor #997e5d
> select clear
> select #5/B:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> color sel #747e5a atoms
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #747e5a
> color sel #00aa7f atoms
> color sel #00aa00 atoms
> color sel #008d00 atoms
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #008d00
> color sel #55aa7f atoms
> color sel #55aa00 atoms
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #55aa00
> color sel #428300 atoms
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #428300
> color sel #442288 atoms
> color sel #aa88bb atoms
> color sel #a8b483 atoms
> ui mousemode right "move label"
[Repeated 2 time(s)]
> select clear
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #428300
> label delete residues
> label #5/B:44-46,20,85,73,49 height 0.6 color white bgColor #428300
> ui mousemode right "move label"
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> label #5/A:270,125,127-130,272 height 0.6 color white bgColor #997e5d
> ui mousemode right "move label"
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!5 models
> select #5/B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5/B:1-15
274 atoms, 278 bonds, 15 residues, 1 model selected
> select #5/B:20
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #5/B:20
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #5/B:21
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> style sel stick
Changed 22 atom styles
> show sel atoms
> hide sel atoms
> select #5/A:98
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #5/A:99
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/A:98
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
202 atoms, 202 bonds, 13 residues, 1 model selected
> style sel stick
Changed 202 atom styles
> show sel atoms
> hide sel atoms
> ui mousemode right "move label"
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> ui tool show "Side View"
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> select #5/B:51
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:51-52
48 atoms, 51 bonds, 2 residues, 1 model selected
> select #5/B:49
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/B:49
24 atoms, 25 bonds, 1 residue, 1 model selected
> hide #!5 models
> show #!1 models
> ui mousemode right distance
> distance #1/B:83@NE2 #1/A:130@OD2
Distance between csJ245rsr86-coot-1.pdb #1/B GLN 83 NE2 and /A ASP 130 OD2:
4.095Å
> distance #1/A:128@OD2 #1/B:15@NH2
Distance between csJ245rsr86-coot-1.pdb #1/A ASP 128 OD2 and /B ARG 15 NH2:
2.801Å
> distance #1/A:130@OD1 #1/B:15@NH1
Distance between csJ245rsr86-coot-1.pdb #1/A ASP 130 OD1 and /B ARG 15 NH1:
3.940Å
> distance #1/B:15@NE #1/A:98@OG1
Distance between csJ245rsr86-coot-1.pdb #1/B ARG 15 NE and /A THR 98 OG1:
3.510Å
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> ui mousemode right "move label"
> ui mousemode right distance
[Repeated 1 time(s)]
> show #!5 models
> hide #!1 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel #55aa00 pseudobonds
> color =sel #00aa7f pseudobonds
> color =sel #00aa00 pseudobonds
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> show #!1 models
> hide #!5 models
> ui tool show "Selection Inspector"
> show #!5 models
> hide #!1 models
> ui tool show "Selection Inspector"
> color =sel forestgreen pseudobonds
[Repeated 1 time(s)]
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel forestgreen pseudobonds
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel forestgreen pseudobonds
> select clear
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel cyan pseudobonds
> color =sel #00aaff pseudobonds
> hide #!5 models
> show #!1 models
> show #3 models
> hide #!1 models
> hide #3 models
> show #!4 models
> show #!1 models
> show #!5 models
> hide #!1 models
> hide #!4 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel forestgreen pseudobonds
> color =sel cyan pseudobonds
> color =sel #00aaff pseudobonds
> select clear
[Repeated 1 time(s)]
> ui tool show "Selection Inspector"
> color =sel #55ffff pseudobonds
> color =sel springgreen pseudobonds
> color =sel cyan pseudobonds
> select clear
> ui tool show "Selection Inspector"
> color =sel forestgreen pseudobonds
> color =sel cyan pseudobonds
> select clear
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> select clear
> show #!1 models
> hide #!5 models
> ui tool show "Selection Inspector"
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel cyan pseudobonds
[Repeated 1 time(s)]
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel cyan pseudobonds
> select clear
> size =sel pseudobondRadius 0.075
Changed 1 pseudobond radii
> color =sel cyan pseudobonds
> select clear
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> label #1/B:15,43,44,70,83 height 0.6 color teal bgColor #ffff7f
> label #1/A:270,127-130,98 height 0.6 color teal bgColor powderblue
> ui mousemode right "move label"
[Repeated 1 time(s)]
> select clear
> ui mousemode right distance
> select clear
> ui mousemode right "move label"
> select clear
> hide #!2 models
> show #!2 models
> select clear
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right select
Drag select of 1 residues
> select clear
Drag select of 1 residues
> ui mousemode right "move label"
> select clear
> ui mousemode right "move label"
> select clear
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> hide #!1 models
> show #!5 models
> label #5/B:73height 0.6 color white bgcolor #428300
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label #5/B:73 height 0.6 color white bgColor #428300
> ui mousemode right "move label"
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
——— End of log from Fri Dec 17 22:27:34 2021 ———
opened ChimeraX session
> hide #5/B:44
> ~label #5/B:44
> ui mousemode right distance
> distance #5/B:73@NE1 #5/A:128@OD1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 NE1 and /A ASP 128
OD1: 3.850Å
> ~distance #1/B:70@NE1 #1/A:128@OD1
> ~distance #5/B:73@NE1 #5/A:128@OD1
> save "E:/temp/EM data/HIV2_HomoModel/HIV2A3G_HM2.cxs"
> distance #5/B:73@NE1 #5/A:128@OD1
Distance between HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B TRP 73 NE1 and /A ASP 128
OD1: 3.850Å
> ~distance #5/B:73@NE1 #5/A:128@OD1
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> swapaa interactive #5/B:20
Missing or invalid "resType" argument: Expected a text string
> swapaa interactive #5/B:20 GLU
HIV2VifCBFbhA3G_HM2-coot0.pdb #5/B GLU 20: phi -59.5, psi -43.8 trans
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4.dev202112170201\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.4.dev202112170201\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4.dev202112170201\bin\lib\site-
packages\chimerax\swap_res\cmd.py", line 134, in rotamers
size(session, rot_objects, stick_radius=0.1)
File "C:\Program Files\ChimeraX 1.4.dev202112170201\bin\lib\site-
packages\chimerax\std_commands\size.py", line 61, in size
is_delta, amount = stick_radius
TypeError: cannot unpack non-iterable float object
TypeError: cannot unpack non-iterable float object
File "C:\Program Files\ChimeraX 1.4.dev202112170201\bin\lib\site-
packages\chimerax\std_commands\size.py", line 61, in size
is_delta, amount = stick_radius
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: NVIDIA GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,261,569,536
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('zh_TW', 'cp950')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.32
ChimeraX-AtomicLibrary: 5.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202112170201
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.1
ChimeraX-ModelPanel: 1.3.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.7.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.15.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.24
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Rotamers calls changed size() directly |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Yen-Li,
--Eric